Evaluation of the Bacterial Diversity of Inner Mongolian Acidic Gruel Using Illumina MiSeq and PCR-DGGE

As a traditional fermented cereal, Inner Mongolian acidic gruel has a unique flavor and rich nutrition, but the microbial diversity of acidic gruel and the microbial differences among the products in different regions have not been reported. The bacterial diversity and the lactic acid bacteria species of 27 types of traditional handmade acidic gruel were evaluated using a combination of MiSeq high-throughput sequencing and PCR-DGGE. All 358,205 high-quality 16S rRNA reads were divided into 25,171 OTUs under the similarity of 97%. Firmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla, and the core dominant genera were Lactobacillus and Acetobacter with average relative abundances of 64.06% and 24.13%, respectively. The primary genera that caused the differences in the bacterial community structure between the Bayan Nur and Ordos acidic gruel samples were Pseudomonas, Leuconostoc, and Acinetobacter as revealed by redundancy analysis (RDA). PCR-DGGE analyses revealed that the lactic acid bacteria in both the Bayan Nur and Ordos samples of acidic gruel were Lactobacillus (L.) amylolyticus, L. alimentarius, L. fermentum, L. hamsteri, L. helveticus, L. panis, L. plantarum, L. pontis, and Leuconostoc lactis. In addition, L. hamsteri was the core strain detected among all the samples. The results deepened the understanding of the microbial community composition and the diversity of acidic gruel to provide a theoretical basis for the preservation and protection of microbial resources in acidic gruel in the Inner Mongolia area.